Chief executive Mark Carne revealed during evidence to the House of Commons public accounts committee how costs had spiralled.
“Fundamentally, our cost estimates were wrong,” he admitted.
He said the latest estimate for costs is between £2.5bn and £2.8bn, but he could not guarantee they would not go higher still. Previous estimates for the project were £874m in January 2013 and £1.6 billion in September 2014.
The public accounts committee is expected to publish its findings into the electrification project before the end of 2015.